Taking screenshots during cutscenes sometimes invokes glitches like this one, where an image of the portal appears in the shot where it does not on the screen.

Presumably forces operating at the Ark began construction of Installatino 04's replacement shortly after the original was destroyed. The undertaking must have been massive. Even so, by the time the events of Halo 3 occur, the reconstruction is not entirely complete.

The Pelican carrying MC and the Arbiter to Installation 04a passes the Elite-controlled Covenant cruiser Shadow of Intent, commanded by Half-Jaw, preparing to leave the Ark and return to Earth through the portal.

The pelican bearing the Master Chief and the Arbiter to Installation 04a passes the Forward Unto Dawn, preparing to land near the control room.

Johnson doesn't do a great job with the splazer. He'll often miss fast-moving targets by failing to lead, and does not take into account intervening obstacles... such as the ledge he is standing on.